13-81895010-A-G

Variant names:

• chr13-81895010-A-G
• rs7318037

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.593 in 151,826 control chromosomes in the GnomAD database, including 27,832 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27832 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90043 AN: 151706 Hom.: 27815 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.633

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.593 AC: 90108 AN: 151826 Hom.: 27832 Cov.: 31 AF XY: 0.595 AC XY: 44177 AN XY: 74230

African (AFR) AF: 0.410 AC: 16977 AN: 41402

American (AMR) AF: 0.648 AC: 9864 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2046 AN: 3464

East Asian (EAS) AF: 0.888 AC: 4585 AN: 5164

South Asian (SAS) AF: 0.699 AC: 3367 AN: 4816

European-Finnish (FIN) AF: 0.635 AC: 6713 AN: 10576

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44443 AN: 67866

Other (OTH) AF: 0.636 AC: 1340 AN: 2108

Alfa AF: 0.632 Hom.: 49759

Bravo AF: 0.590

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7318037; hg19: chr13-82469145;